New element: "Convert SnpEff Variations to Annotations". Element converts variations with SnpEff information into standard annotations, so you can observe them in the Sequence View.

NGS workflows improvements.

Bug fixes.

July 8th, 2016 : UGENE 1.23.1 has been released

This is a patch release that contains several major bug fixes

June 25th, 2016 : UGENE 1.23.0 has been released

Major changes in this release include:

Auto-update: there is no need to download a new version manually anymore. As soon as the new version released, UGENE will ask your permission to update and with your consent the program will be updated automatically.

Usability: Ctrl+V in the Project View was supported.
For example, if you have a sequence in the FASTA format, opened in a text editor, try to:

Select the text of the sequence. Press Ctrl+C.

Open UGENE and activate the Project View. Press Ctrl+V.

You should see that a new document has been created with the corresponding data.

Note that this feature is supported for other formats as well.

In silico PCR: a possibility to include annotations to the extracted PCR product was added.

Sequence View: exporting of a sequence image was improved. It is now possible to export the Details View and the Zoom View separately in different formats, including SVG.

NGS: partially valid VCF files can now be opened. A warning notification is shown for lines that can’t be parsed.

Usability: some buttons from a toolbar of the Sequence View were moved to the left toolbars of the sequence sub-views: Zoom View, Details View, etc.

Usability: a new icon for a circular sequence was added to the Project View.
When you work with a circular sequence, don’t forget to check “Mark as circular” in the Project View. In this case all algorithms in the Sequence View will take into account that the sequence is circular.

Optimizations of big data processing in UGENE.

The full list of changes done in this release can be found in our bug tracker.

July 7th, 2015 : UGENE 1.17.0 has been released

Important changes in this major release include:

Sequence View: recalculation of regions in qualifiers after sequence editing

"Here we present NGS pipelines “Variant Calling with SAMtools”, “Tuxedo Pipeline for RNA-seq Data Analysis” and “Cistrome Pipeline for ChIP-seq Data Analysis” integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters."

October 8th, 2014 : UGENE 1.14.2 has been released

This is a patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

The webinars are mostly useful to people with small experience in using UGENE or without the experience at all. However, experienced users may also find them useful, as they provide some tips on using UGENE.

Approximate plan of the webinars is the following:

UGENE basics

Analyzing a sequence

Multiple sequence alignment

In addition, each webinar will take into account preferences of the participants. The participants will also be able to ask questions throughout the webinar. The webinars are free of charge.

Shared storage: sharing of bioinformatics data in a lab. For details, see this page.

Alignment Editor:

Overview for a multiple alignment was added, a lot of configuration options are available.

A multiple alignment consensus can now be exported.

Phylogenetic Trees:

PhyML Maximum Likelihood was integrated.

It is now possible to re-root a tree.

Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.

Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

February 12th, 2014 : UGENE 1.13.1 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

December 11th, 2013 : UGENE 1.13.0 is released

Important changes in this major release include:

DAS: you can now annotate an unknown amino acid sequence using annotations of its homologs. First, you search for homologs using the Uniprot BLAST. Second, you load the annotations of the selected homologs to your sequence using the Distributed Annotation System (DAS).

The full list of changes done in this release can be found in our bug tracker

March 7th, 2013 : UGENE 1.11.5 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

December 26th, 2012 : UGENE 1.11.4 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

November 2nd, 2012 : UGENE 1.11.3 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

October 1st, 2012 : UGENE 1.11.2 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

August 6th, 2012 : UGENE 1.11.1 is released

This is patch release that contains several major bug fixes and minor interface improvements requested by users

The full list of changes done in this release can be found in our bug tracker

May 26th, 2012 : UGENE 1.11.0 is released

The latest UGENE 1.11 version is a major release that provides dozens of new features (major and minor), bug fixes and a set of usability and other improvements.

The major changes are:

The Sequence View was extended with an options panel. It shows interactive information about a selected sequence region, allows you to easily set up the annotation types' properties (for example annotations' colors) and to search for a pattern in a sequence.

You can now calculate a consensus sequence for assembly data in the Assembly Browser, using either a simple default algorithm or an algorithm from SAMtools. Also, it is now possible to highlight paired reads and SNP in assembly data. Another minor handy feature is the possibility to add bookmarks in the Assembly Browser.

To create more sophisticated workflows in the Workflow Designer you can use new data flow elements Grouper and Multiplexer.

An mRNA-to-genomic alignment program Spidey was embedded into UGENE as an external tool.

UGENE 64-bit version is now available for Windows.

To overview the changes you can watch "Whats new in UGENE 1.11" podcast episode. The full list of changes can be found in the bug tracker.

The full list of changes done in this release can be found in our bug tracker

Our team member Konstantin Okonechnikov gave a talk about UGENE during the Genome Content Management section. You can see him on the picture below with people from other open-source bioinformatics projects.

From left to right: James B.Procter(JalView), Peter Cock(Biopython), Konstantin Okonechnikov(UGENE) and Peter Troshin (JABAWS).

BOSC proceddings including UGENE project abstract can be downloaded from here.

July 25th, 2011 : UGENE 1.9.5 and changes in the release cycle

UGENE team is glad to announce a major change in the release cycle which will allow to improve stability and reliablity of the bioinformatics toolkit.

From now on we are going to ship hot-fix releases every time a major bug is discovered. Such releases can be distinguished by the third digit in the version nuber. You can read more about the new versioning system in the following forum thread.

As we mentioned earlier, UGENE project participated in the Illumina iDEA Challenge 2011. The contest was devoted to analysis and visualization of the data generated by Illumina technologies in the context of cancer genome research. For this challenge we presented the UGENE Assembly Browser, a neat BAM viewer.

The final of Illumina iDEA 2011 challenge took place in San Diego, CA, USA on the 14-15th June 2011. During the Illumina iDEA 2011 conference the finalists and guest scientists gave their talks about future of Next Generation Sequencing.

Our team member Mikhail Fursov was representing UGENE on this event.

June 3rd, 2011 : Workshop on UGENE was held in Novosibirsk State University

A training workshop on UGENE organized by Unipro and Novosibirsk State University was held between the 30th May and 2nd June. A group of young biologists from several Siberian universities and research labs gathered together to study on how to work with UGENE and use the toolkit in their everyday research.

The workshop covered various topics in bioinformatics: homology searching in databases, performing multiple alignment, working with NGS data and much more. An important goal of the workshop was to familiarize scientists with the usage of high-performance computing. The participants also learned the innovative concepts of Workflow Desinger and Query Designer. The lectures and tutorial sessions were conducted by UGENE team members and experienced scientists from NSU and local research institutions.

The workshop was supported by a grant from Russian Federal Targeted Program пїЅR&D in Priority Fields of the S&T Complex of RussiaпїЅ.

May 23rd, 2011 : UGENE 1.9.3 is released

Starting from this version UGENE provides advanced support for NGS data analysis. The most notable feature of current release is the Assembly Browser, a powerful GUI tool to visualize BAM files. It was tested against data from 1000 Genomes project, Illumina iDEA Challenge and data from other sources. Find out more about Assembly Browser in UGENE user manual.

The new version also includes multiple improvements and bugfixes. Here are some of them:

Sequence View: added functionality to manage number of visible rows in Zoom View

We are pleased to announce that Unipro UGENE project won award in the contest "Efficient Use of GPU-Accelerators to Solve Large Problems". The contest is held by T-Platformscompany – a leading provider of high-performance computing systems in Russia and Europe.

The contest consists of several parts. In the first part each participant presented a detailed description of a scientific project in the area of GPU computing. The winners of the first part will now start working on the implementation of the project. As part of this contest a new feature will be included into UGENE: fast assembly of NGS data using modern GPUs.

March 24th, 2011 : UGENE 1.9.2 is released

New version includes several critical bug fixes and some new features:

UGENE Genome Aligner is optimized towards better performance. Now it can use modern GPUs to boost the computations

Automatic annotation highlighting for Restriction Enzymes plugin is introduced. Once configured, restriction sites search is performed for newly opened sequences automatically — no need to launch search every time for new molecule.

From now on UGENE users don't need to search and manually install supported external tools. Follow this link to download "all-in-one" external-tools pack.

December 25th, 2010 : Development snapshots are available

Great news for those who are impatient to check new features of UGENE before official release! From now on the latest unstable snapshots are available from our web-site.

The development snapshots include MS Windows, Linux and source packages. Please note that Windows binary snapshot is represented as portable zip archive: just unpack it to any directory and launch ugeneui.exe.

We are happy to announce that Unipro UGENE project was honored as Best Open-Source Project in Russian Federation. The annual contest is held by Linux Format magazine with the support of Intel, PingWin Software, IBM developerWorks and GNU/Linuxcenter companies. About 100 participants took part in the contest this year.

UGENE team is proud to win the award and we want to thank all our users for help and support! Without your useful suggestions and feedback UGENE wouldn't get this far.

We are planning to make our project 200% better and win more awards next year 🙂

December 15th, 2010 : UGENE 1.9.0 is released

Meet the hot new UGENE release! Originally we planned to roll out version 1.8.1, but the new version includes so many new features that we decided to name it 1.9.0.

The release includes:

Support for "cloning in silico". From now on it is possible to automatically digest sequences into fragments and construct new molecules from defined fragments. This functionality is the first step to fully support cloning feature, which is one of the top requests from UGENE users. For detailed overview of new functionality check out thistutorial available from UGENE User Manual.

The release also includes multiple minor improvements and bugfixes. The full changelist is available here. Thanks to your feedback UGENE is becoming better and better — most of the current bugfixes are initiated by our users.

November 3rd, 2010 : UGENE wins award at contest held by Intel and Rusnano

This year Unipro UGENE project participated in the High Performance Computing contest held by Rusnano and Intel corporations. The main goal of the HPC-2010 contest was to determine best academic projects in Russia in the area of scientific computing.

About 100 projects took part in the contest. Most of them were strong and promising. In result UGENE won the Bronze Third Place award.

In version 1.8.0 we decided to give up old Remote Task protocol model. From now on all remote tasks are exectued only via UGENE remote service based on Amazon EC2. The UGENE remote service is ready for testing.

August 20th, 2010 : UGENE 1.7.2 is released

UGENE team is glad to announce UGENE 1.7.2. The new version includes several awesome new features and numerous enhancements.

New features:

Launch your computational tasks on Amazon EC2 with UGENE! The release includes experimental support for cloud computing.

Support for external tools: now Clustal and Mafft alignment available in UGENE.

New format is supported: Nexus

UGENE documentation is being reworked and improved. From now on UGENE user manual is available as printable PDF.

Improvements and bugfixes:

Multiple Alignment Editor: delete columns with relative number of gaps;

A lot of improvements were made to console version of UGENE. It has become much more flexible and powerful. Since now it is possible to use command line version of UGENE in complex scripts and shell scenarios. There are useful prebuilt scenarios available: align, convert, find repeats etc.

Other cool features available:

New advanced sequence analysis algorithm based on weight matrices;

Circular view improvements: zoooming, rotating and more;

Support for advanced search options of NCBI BLAST in redesigned Remote Request plugin.

UGENE team is glad to announce that beginning from today, users of PowerPC-based Macs can use our software right out of the box. Feel free to check the downloads page for the new Mac universal package which is able to run on both x86 and ppc platforms.

July 17th, 2009 : UGENE 1.5.1 released

UGENE v 1.5.1 is a bug fix release which is strongly recommended to install since it fixes several serious issues.

Please note, that before installing v1.5.1 (or v1.5.0) it is required to completely remove any previous installations of UGENE.

New plugins:

BALL – adds new types of molecular surfaces to UGENE 3D viewer

New features and bug fixes:

New feature: sequence line view and MSA editor now support saving fancy screenshots

UGENE has been presented at The Fifth Moscow International Congress "Biotechnology: State of the Art and Prospects of Development" and the VII International Specialized Exhibition "Biotech World' 2009"

Also UGENE has been presented at PaVT' 2009( official russian web site ) – an international conference devoted to parallel computing. It was held in Nizhny Novgorod, Russia.

Poster and computer presentation "New multitasking software system for real-time analysis of genomic sequences" devoted to UGENE project use cases and perspectives was held at"Molecular Oncology" conference.

The conference was organized at Novosibirsk by branch of Russian Academy of Medical sciences. link

September 19th, 2008 : UGENE v1.2.0 is released

Unipro UGENE v1.2 is the next minor release of the product.

It adds several new plugins, MacOS X platform support and dozens of performance, usability and compatibility improvements.

UGENE v1.1.1 is bug fix only release. It includes set of performance, stabilty and compatibility improvements made since the release of version 1.1.0 in July 2008.

July 22nd, 2008 : Unipro releases UGENE v1.1

This version adds HMMER package integration, support for compressed files and fixes several usability and performance issues. The complete list of changes can be found here.

June 23rd, 2008 : BGRS 2008 conference

Unipro UGENE team participated in "The Sixth International Conference on Bioinformatics of Genome Regulation and Structure" (BGRS'2008) with a computer demonstration in "High Performance Computing in Bioinformatics" section.

June 17th, 2008 : The first version of Unipro UGENE

We proud to announce the first version of Unipro uGENE project for Solaris and Windows operating systems.